Hello
98% is at the reconfiguration stage. If your sole purpose is to shrink the disk, you don't need reconfiguration. It can be switched off in the wizard. To be on the safe side check that your converter version supports files that large (5.5 or 6.0 is OK, perhaps older too)
As for the running conversion - if you cancel it, that should be OK - you could use the disk. However if it has is stuck, perhaps canceling would perhaps not finish too. Stopping the converter worker service will finish the conversion of course but you can't rely on the disk integrity in that case.
HTH
Plamen